Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA.
Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA.
Cell. 2018 Oct 18;175(3):877-886.e10. doi: 10.1016/j.cell.2018.09.044.
Biological signaling networks use feedback control to dynamically adjust their operation in real time. Traditional static genetic methods such as gene knockouts or rescue experiments can often identify the existence of feedback interactions but are unable to determine what feedback dynamics are required. Here, we implement a new strategy, closed-loop optogenetic compensation (CLOC), to address this problem. Using a custom-built hardware and software infrastructure, CLOC monitors, in real time, the output of a pathway deleted for a feedback regulator. A minimal model uses these measurements to calculate and deliver-on the fly-an optogenetically enabled transcriptional input designed to compensate for the effects of the feedback deletion. Application of CLOC to the yeast pheromone response pathway revealed surprisingly distinct dynamic requirements for three well-studied feedback regulators. CLOC, a marriage of control theory and traditional genetics, presents a broadly applicable methodology for defining the dynamic function of biological feedback regulators.
生物信号网络利用反馈控制实时动态调整其运作。传统的静态遗传方法，如基因敲除或挽救实验，通常可以识别反馈相互作用的存在，但无法确定所需的反馈动态。在这里，我们实施了一种新策略，闭环光遗传学补偿（CLOC），来解决这个问题。使用定制的硬件和软件基础设施，CLOC 实时监测被反馈调节剂删除的途径的输出。一个最小模型使用这些测量值来计算并实时提供一个光遗传学激活的转录输入，旨在补偿反馈删除的影响。CLOC 在酵母信息素反应途径中的应用揭示了三个研究充分的反馈调节剂的惊人不同的动态要求。CLOC 是控制理论和传统遗传学的结合，为定义生物反馈调节剂的动态功能提供了一种广泛适用的方法。
